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| Operon |  |
|---|---|
| Name: | yceD-rpmF-plsX-fabHDG-acpP-fabF |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | yceD-rpmF | ||||||
| Gene(s): | yceD, rpmF Genome Browser M3D Gene expression COLOMBOS | ||||||
| Note(s): | FNR represses yceD gene expression under anaerobiosis, but it is not known which of the two promoters transcribing the gene is affected, or even if this regulation is direct or indirect Salmon K,2003. | ||||||
| Evidence: | [LTED] Length of transcript experimentally determined | ||||||
| Reference(s): | [1] Tanaka Y., et al., 1989 | ||||||
| Promoter | |||||||
| Name: | yceDp1 | ||||||
| +1: | 1146649 | ||||||
| Distance from start of the gene: | 145 | ||||||
| Sequence: |
| Note(s): |
This promoter appears to have more transcriptional sites at positions 1146648/49/50 , as determined by high-throughput screening of maps of promoters Lacoux C,2020. |
Evidence: |
[CV(RS-EPT-CBR)] |
[CV(TIM)] [HIPP] [RS-EPT-CBR] [TIM] Reference(s): |
[2] Salgado H, et al., 2012 |
[1] Tanaka Y., et al., 1989 |
| Name: | yceD-rpmF | ||||
| Gene(s): | yceD, rpmF Genome Browser M3D Gene expression COLOMBOS | ||||
| Note(s): | FNR represses yceD gene expression under anaerobiosis, but it is not known which of the two promoters transcribing the gene is affected, or even if this regulation is direct or indirect Salmon K,2003. | ||||
| Evidence: | [LTED] Length of transcript experimentally determined | ||||
| Reference(s): | [1] Tanaka Y., et al., 1989 | ||||
| Promoter | |||||
| Name: | yceDp2 | ||||
| +1: | 1146791 | ||||
| Distance from start of the gene: | 3 | ||||
| Sequence: |
| Evidence: |
[CV(RS-EPT-CBR)] |
[CV(TIM)] [HIPP] [RS-EPT-CBR] [TIM] Reference(s): |
[2] Salgado H, et al., 2012 |
[1] Tanaka Y., et al., 1989 |
| Name: | rpmF-plsX-fabHDG |
| Gene(s): | rpmF, plsX, fabH, fabD, fabG Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | The rpmF and pslX-fab genes are cotranscribed, and this is the fist example where lipid biosynthetic genes and a ribosomal protein gene comprise an operon Podkovyrov S,1995 It is probable that yceD-rpmF-plsX-fabHDG-acpP-fabF cluster genes are regulated together, since they are involved in the same functional class. However, a transcript that continues through the entire gene cluster has not been determined by Northern blotting or by experiments with polar mutations. |
| Evidence: | [PM] Polar mutation |
| Reference(s): | [3] Podkovyrov S., et al., 1995 |
| Promoter | |
| Name: | rpmFp |
| +1: | 1147338 |
| Distance from start of the gene: | 29 |
| Sequence: |
acccatttgccgtattagccagcttaaagcgtaagtaattggtgctccccgttggatcggGgataaaccgtaattgaggag |
| Evidence: | [HTIM] |
| Reference(s): | [4] Mendoza-Vargas A., et al., 2009 |
| Name: | plsX-fabHDG |
| Gene(s): | plsX, fabH, fabD, fabG Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | The pslX transcripts were detected only by RT-PCR, and therefore the lengths of these transcripts are unknown. They could initiate at the promoters located upstream of g30k as determined by Tanaka Y,1989and/or at the fabH promoter mapped by Podkovyrov SM,1996CITS:[9642179]|. It is probable that yceD-rpmF-plsX-fabHDG-acpP-fabF cluster genes are regulated together, since they are involved in the same functional class. However, a transcript that continues through the entire gene cluster has not been determined by Northern blotting nor by experiments with polar mutations. |
| Evidence: | [PM] Polar mutation |
| Reference(s): | [5] Zhang Y., et al., 1998 |
| Promoter | |
| Name: | plsXp |
| +1: | 1147577 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 44 |
| Sequence: |
ggccgcaaggtcatcgctaagtaatcacgcatctgcgtgatgaagcttagtgaggattttCcccaggcaactggggaaaga -35 -10 +1 |
| Evidence: |
[ICWHO] [TIM] |
| Reference(s): | [6] Thomason MK., et al., 2015 |
| Name: | fabHDG | ||||||
| Gene(s): | fabH, fabD, fabG Genome Browser M3D Gene expression COLOMBOS | ||||||
| Note(s): | This transcription unit is part of a group of genes (encoding acyl carrier protein and several key fatty acid biosynthetic enzymes) which are not transcribed as a classic operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene. The fabHGD operon is subject to stringent control Podkovyrov SM,1996 |
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| Evidence: | [PAGTSBP] Products of adjacent genes in the same biological process | ||||||
| Reference(s): | [7] Podkovyrov SM., et al., 1996 | ||||||
| Promoter | |||||||
| Name: | fabHp | ||||||
| +1: | 1148516 | ||||||
| Distance from start of the gene: | 243 | ||||||
| Sequence: |
| Note(s): |
fabHp is subject to stringent control, and it is responsible for ~40% of all transcripts for fabH Podkovyrov SM,1996 |
fabH has a GC-rich motif discriminator sequence between the -10 region and the start site, which is a characteristic feature of the stringently regulated promoter Podkovyrov SM,1996 The fabH promoter is not only a contributor to its expression under all conditions, but also other activators might compensate to activate fabH expression when FadR is absent, and/or with basal expression of the fabHGD genes My L,2013 Evidence: |
[TIM]
|
Reference(s): |
[7] Podkovyrov SM., et al., 1996
|
|
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | FadR | activator | fabHp | 1148470 | 1148486 | -38.0 | attcagtcacCTCAACCCCGACCAGTAtaacggcgcc | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [8], [9] |
| Allosteric regulation of RNA-polymerase |
| Regulator | Function | Promoter target of RNApol | Growth Conditions | Note | Evidence | Reference | |
|---|---|---|---|---|---|---|---|
| DksA-ppGpp | inhibition | fabHp | ppGpp and its cofactor, DksA, inhibit in two ways the transcription of fabHp: 1) they directly inhibit its transcription, and 2) they inhibit fadR expression, which is an activator of the fabHDG operon My L,2013 | [GEA] |
[8] [7] |
| Evidence: | [GEA] Gene expression analysis |
| Reference(s): |
[8] My L., et al., 2013 [7] Podkovyrov SM., et al., 1996 |
| Name: | acpP-fabF |
| Gene(s): | acpP, fabF Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | This transcription unit is part of a group of genes (encoding acyl carrier protein and several key fatty acid biosynthetic enzymes) which are not transcribed as a classic operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene Zhang Y,1996. |
| Evidence: | [LTED] Length of transcript experimentally determined |
| Reference(s): | [10] Zhang Y., et al., 1996 |
| Promoter | |
| Name: | acpPp |
| +1: | 1151575 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 40 |
| Sequence: |
atcgtggtaagacctgccgggatttagttgcaaatttttcaacattttatacactacgaaAaccatcgcgaaagcgagttt |
| Note(s): | acpPp is the major transcription start site for the acpP-fabF operon; however, there is a minor signal for this 1 nt downstream of the acpPp promoter Zhang Y,1996. |
| Evidence: |
[HIPP] [TIM] |
| Reference(s): | [10] Zhang Y., et al., 1996 |
| Name: | acpP |
| Gene(s): | acpP Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | acpP expression is not under growth rate control Zhang Y,1996. A consensus sequence resembling the FadR-binding site was identified at position -40 upstream from the acpP promoter Henry MF,1992. However, analysis in a gel shift assay of the acpP fragment containing the putative FadR-binding site compared to the purified FadR protein gave no significant shift of the DNA band, nor was there a significant change in acpP expression in a fadR null mutant strain. These findings indicate that FadR is not involved in the regulation of ACP expression Zhang Y,1996. |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified [LTED] Length of transcript experimentally determined |
| Reference(s): |
[11] Rawlings M., et al., 1992 [10] Zhang Y., et al., 1996 |
| Promoter | |
| Name: | acpPp |
| +1: | 1151575 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 40 |
| Sequence: |
atcgtggtaagacctgccgggatttagttgcaaatttttcaacattttatacactacgaaAaccatcgcgaaagcgagttt |
| Note(s): | acpPp is the major transcription start site for the acpP-fabF operon; however, there is a minor signal for this 1 nt downstream of the acpPp promoter Zhang Y,1996. |
| Evidence: |
[HIPP] [TIM] |
| Reference(s): | [10] Zhang Y., et al., 1996 |
| Terminator(s) | |
| Type: | rho-independent |
| Sequence: | aagtgaacatCTCCAGGCGGTCGTTCGACCGCCTGAGTtttatctttt |
| Reference(s): | [11] Rawlings M., et al., 1992 |
| Name: | fabDG-acpP |
| Gene(s): | fabD, fabG, acpP Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | This transcription unit is part of a group of genes (encoding acyl carrier protein and several key fatty acid biosynthetic enzymes) which are not transcribed as a classic operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene. |
| Evidence: | [LTED] Length of transcript experimentally determined |
| Reference(s): | [10] Zhang Y., et al., 1996 |
| Name: | fabF |
| Gene(s): | fabF Genome Browser M3D Gene expression COLOMBOS |
| Evidence: | [LTED] Length of transcript experimentally determined |
| Reference(s): | [10] Zhang Y., et al., 1996 |
| Name: | fabG-acpP |
| Gene(s): | fabG, acpP Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | This transcription unit is part of a group of genes (encoding acyl carrier protein and several key fatty acid biosynthetic enzymes) which are not transcribed as a classic operon, but rather multiple promoters are present and each gene is cotranscribed with at least one other gene. |
| Evidence: | [LTED] Length of transcript experimentally determined |
| Reference(s): |
[11] Rawlings M., et al., 1992 [10] Zhang Y., et al., 1996 |
| RNA cis-regulatory element | |
|---|
| Regulation, transcriptional elongation | |
| Attenuator type: | Transcriptional |
| Strand: | forward |
| Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
|---|---|---|---|---|---|
| terminator | -18.3 | 1151860 | 1151900 | agtgaacatcTCCAGGCGGTCGTTCGACCGCCTGAGTTTTATCTTTTTGTcccactagaa | |
| terminator | -11.6 | 1151568 | 1151601 | ttttatacacTACGAAAACCATCGCGAAAGCGAGTTTTGATAGgaaatttaag | |
| anti-terminator | -12.3 | 1151834 | 1151874 | gattacatcaACGGCCACCAGGCGTAAGTGAACATCTCCAGGCGGTCGTTcgaccgcctg | |
| anti-anti-terminator | -10.5 | 1151809 | 1151848 | aatcaccaccGTTCAGGCTGCCATTGATTACATCAACGGCCACCAGGCGtaagtgaaca |
| Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
| Reference(s) |
|
|---|---|
[CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)